Hi Conrad, I will see if I can change to POST. To explain a bit: Jalview (Java) application uses POST, we now have a Javascript version which for the moment is limited to sending GET requests, so I tweaked the code for that. I will see if I can persuade it to fake a POST instead and let you know what I find. Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs@dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 ________________________________ From: Conrad Huang <conrad@cgl.ucsf.edu> Sent: 04 February 2019 21:21:12 To: Mungo Carstairs (Staff); chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Help: 'broken pipe' error Hi, Mungo. I tried using the RESTserver on a recent daily build, and it opening 4zhp worked fine. Since RESTserver hasn't changed in a very long time, I suspect the results would be the same with 1.13. The way I tested it is to start the RESTserver in Chimera, and then go to a browser to visit "http://localhost:PORT/static/cmdline.html" where PORT is the port number reported in the Reply Log. A form is displayed in the browser and I type in "open cifID:4zhp", which runs the command and displays Chimera messages in the browser rather than the Reply Log. I did notice that your tests show messages like:
127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 -
whereas mine show:
127.0.0.1 - - [04/Feb/2019 12:02:46] "POST /run HTTP/1.1" 200 -
That looks to me like you are sending requests using http GET, whereas my tests are using POST. It /shouldn't/ make any difference, but would it be possible for you to test using POST to send requests to Chimera instead of GET? Conrad On 2/1/2019 2:43 AM, Mungo Carstairs (Staff) wrote:
Hi there,
I'm experimenting with Jalview /as Javascript/ talking to Chimera over the latter's REST server.
The first few 'list models' commands work fine, but when I send a command 'open cifID:4zhp' I (usually but not always) get an error '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces below as to the reason for this? Thanks.
Chimera 1.12 (build 41481) on OSX Sierra 10.12.6.
REST server on host 127.0.0.1 port 53135 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 - Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread callable() File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run _run(q, h, args) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 163, in _run replyobj.error(str(v) + '\n') File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 637, in error _replyStack[-1].error(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine self.write(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write self.f.write(s) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe thread callback: error: [Errno 32] Broken pipe
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size])
See reply log for Python traceback.
---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 53326) Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request self.finish_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 - Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", line 50, in _checkThread callable() File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 83, in run _run(q, h, args) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 159, in _run chimera.runCommand(cmd) File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2750, in runCommand makeCommand(*args, **kw) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 69, in makeCommand f(c, args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py", line 20, in command self.module("cmdline").process(cmdName, args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 12, in process doList(args) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 543, in doList doExtensionFunc(func, otherArgs, **kwargs) File "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line 451, in doExtensionFunc extFunc(*tuple(processedArgs), **kw) File "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line 192, in listr replyobj.info(info) File "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line 625, in info _replyStack[-1].info(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 202, in message self.writeLine(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 184, in writeLine self.write(s) File "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", line 191, in write self.f.write(s) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 328, in write self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe thread callback: error: [Errno 32] Broken pipe
File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size])
See reply log for Python traceback.
---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 53329) Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 295, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 321, in process_request self.finish_request(request, client_address) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 657, in __init__ self.finish() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", line 716, in finish self.wfile.close() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 283, in close self.flush() File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20models%20type%20molecule HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 - 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -
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*Mungo Carstairs* Jalview Computational Scientist
The Barton Group Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.jalview.org<http://www.jalview.org> <http://www.jalview.org>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> <http://www.compbio.dundee.ac.uk> g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>
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